X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Temperature Control
pH 7
Temperature 293.0
Details 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentanediol, 500mM CaCl2, pH 7.0, TEMPERATURE CONTROL, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 18.46 α = 90
b = 18.46 β = 90
c = 71.46 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-02-13
Diffraction Radiation
Monochromator Protocol
Fixed exit Si (111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPRING-8 BL38B1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.3 36 99.2 0.072 -- -- 6.6 3879 3859 0.0 0.0 7.49
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.3 1.47 99.7 0.051 -- -- 8.2 539

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.3 23.821 -- 2.92 -- 3832 168 98.79 -- 0.1951 0.1895 0.23 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.3002 13.2757 -- 168 3654 0.1932 0.2323 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.72
Anisotropic B[1][1] 0.5118
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5118
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0236
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 29.929
f_plane_restr 0.006
f_chiral_restr 0.073
f_angle_d 1.862
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 120
Heterogen Atoms 7
Solvent Atoms 41

Software

Computing
Computing Package Purpose
BSS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MANUAL Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
MANUAL model building
BSS data collection